I moved this from the custom firmware thread because this is more of, i suspect, a settings issue.

There are a few possibilities:

1) Extruder temp is too low for the filament
2) Dirt/trash/old filament trapped in the extruder drive gear. You might need to clean it with a wire brush.
3) Too high of extrude settings, or too fast of printing causing the extruder to work harder than it is capable of. IOW, Double check your slicer settings.

I have this problem when the bed is out of alignment. IE the bed is to close to the extruder and it cannot extrude.

To test this theory, lower the corresponding screw to the area where it starts clicking. It should slowly begin to click less and start printing, and then not click at all. This would then confirm you have an alignment issue.

To add to what Keith mentioned, if the extruder is working too hard to keep up (ie it is clicking, which means it is missing steps) on other printers I have checked the amount of current going to the stepper extruder to make sure that it is in the correct range and adjust if necessary. One thing to be careful for is that if you increase the current going to the stepper it increases the amount of heat, which could effect the lifespan of the extruder.

Easiest fixes, in this order;

Check the extrusion temp and make sure it is in the normal range for your filament
Make sure the print head isn't too close to the glass
Slow down the print (The extruder might be able to keep up)
Check for blockages

For those having the clicking - IF it happens into a print (IE, not the first few layers) I would like to know your layer settings. I am now thinking that the extruder might be trying to supply too much plastic, and subsequently "loading" up. At that point the plastic swells in the melt chamber, and 'voila, clicking sarts happening. Its only a guess, but I need more data.

So, if your having clicking, please let me know your slicer settings for layer height. And please try setting it for .4 and let me know if the problem continues.

The clicking happens even when I am extruding into thin air. It doesn't seem to care. I though tit might be Rep so I switched back to 1.1g and it does the same thing. i suspect my heater on the extruder is wrong as it was just replaced due to a broken wire. Any thoughts?

Here is my findings on clicking. Clicking started when I switched to clear ABS from a 3rd party, before that I had only used factory filament and never had clicking problem. At first I thought it was the temperature setting problem, so I played with different temperatures (210 to 230) but to no avail. Then I checked the bed for levelness, turned out fine, so I know its not the bed. I also noticed that there is no filament or very little filament coming out of the nozzle whenever clicking starts, so I tried the filament multiplier setting in slic3r anywhere from 0.9 to 1.2, still the same. Then I suspect the filament gripper in the extruder is losing steps, I took out the extruder and cleaned the pinion gears and clicking is still there. So I started thinking maybe the clear ABS is to be blamed. Then I ordered a white filament from another 3rd party supplier, loaded in and printed the same object, clicking is gone. In my case, the filament quality has a lot to do with clicking problem. I thought I would share my experience with everyone, hopefully that helps.

If you are using clear filament, the reason you may be getting the clicking is due to the optical sensor in the extruder part. You will need to block the sensor that is part of the extruder with something like foil.

Thanks for your advice. I was getting the clicking using clear filament with or without the optical sensor masked. I also read somewhere ,but don't remember where, one possible cause of clicking is hot-end being set to a temperature too high for that particular filament in use and the filament melts before the gear has a chance to push it into the hot-end.